get_biomart: Get Ensembl biomaRt object

Description Usage Arguments

View source: R/functions.R

Description

Get GC content, gene Ids, gene symbols, gene biotypes, gene lengths and other metadata from Ensembl BioMart. Object returned contains gene Ids as rownames.

Usage

1
get_biomart(count_df, gene_id, synid, version, host, filters, organism)

Arguments

count_df

A counts data frame with sample identifiers as rownames.

gene_id

Column name of gene Ids

synid

A character vector with a Synapse Id.

version

Optional. A numeric vector with the Synapse file version number.

host

An optional character vector specifying the release version. This specification is highly recommended for a reproducible workflow. (see "biomaRt::listEnsemblArchives()")

filters

A character vector listing biomaRt query filters. (For a list of filters see "biomaRt::listFilters()")

organism

A character vector of the organism name. This argument takes partial strings. For example,"hsa" will match "hsapiens_gene_ensembl".


jgockley62/UW_RNASeq documentation built on Oct. 1, 2020, 8:07 p.m.